Complete Genome Sequence of NRM_5 Strain Isolated from the Fecal Samples of a Wild Indian Ring-necked Parakeet (is) in Japan

Overview

Journal Microbiol Resour Announc

Publisher American Society for Microbiology

Specialty Microbiology

Date 2024 Apr 29

PMID 38682775

Authors

Yukiko Sassa-OBrien

Chien-Fu Wu

Yasuhiko Matsushita

Kenji Ohya

Hiromitsu Moriyama

Hideto Fukushi

Affiliations

Soon will be listed here.

Abstract

We report here the whole-genome sequence of the NRM_5 strain isolated from the fecal samples of wild Indian ring-necked parakeet () in Japan. The sequence type is ST35, which is known to be associated with pigeons and doves, indicating the potential for transmission among bird species.

References

Jelocnik M, Polkinghorne A, Pannekoek Y . Multilocus Sequence Typing (MLST) of Chlamydiales. Methods Mol Biol. 2019; 2042:69-86. DOI: 10.1007/978-1-4939-9694-0_7. View

Kasimov V, White R, Foxwell J, Jenkins C, Gedye K, Pannekoek Y . Whole-genome sequencing of from Australasian avian hosts: A genomics approach to a pathogen that still ruffles feathers. Microb Genom. 2023; 9(7). PMC: 10438822. DOI: 10.1099/mgen.0.001072. View

Langmead B, Salzberg S . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. PMC: 3322381. DOI: 10.1038/nmeth.1923. View

Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5):455-77. PMC: 3342519. DOI: 10.1089/cmb.2012.0021. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

Jackson H, Strubbe D, Tollington S, Prys-Jones R, Matthysen E, Groombridge J . Ancestral origins and invasion pathways in a globally invasive bird correlate with climate and influences from bird trade. Mol Ecol. 2015; 24(16):4269-85. PMC: 4657503. DOI: 10.1111/mec.13307. View

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

Chu J, Sun R, Wu Z, Liu S, Li D, Zhang Q . Whole-Genome Sequences of Low-Virulence Strain CB3 and Mild Strain CB7 of Chlamydia psittaci. Genome Announc. 2014; 2(3). PMC: 4047443. DOI: 10.1128/genomeA.00456-14. View

Gordon D, Green P . Consed: a graphical editor for next-generation sequencing. Bioinformatics. 2013; 29(22):2936-7. PMC: 3810858. DOI: 10.1093/bioinformatics/btt515. View

10.

Balsamo G, Maxted A, Midla J, Murphy J, Wohrle R, Edling T . Compendium of Measures to Control Chlamydia psittaci Infection Among Humans (Psittacosis) and Pet Birds (Avian Chlamydiosis), 2017. J Avian Med Surg. 2017; 31(3):262-282. DOI: 10.1647/217-265. View

11.

Tanizawa Y, Fujisawa T, Nakamura Y . DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics. 2017; 34(6):1037-1039. PMC: 5860143. DOI: 10.1093/bioinformatics/btx713. View

12.

Kuo C, Chen H, Wang S, GRAYSTON J . Identification of a new group of Chlamydia psittaci strains called TWAR. J Clin Microbiol. 1986; 24(6):1034-7. PMC: 269093. DOI: 10.1128/jcm.24.6.1034-1037.1986. View

13.

Jelocnik M, Jenkins C, ORourke B, Barnwell J, Polkinghorne A . Molecular evidence to suggest pigeon-type Chlamydia psittaci in association with an equine foal loss. Transbound Emerg Dis. 2018; 65(3):911-915. DOI: 10.1111/tbed.12817. View

14.

Van Lent S, Piet J, Beeckman D, van der Ende A, Van Nieuwerburgh F, Bavoil P . Full genome sequences of all nine Chlamydia psittaci genotype reference strains. J Bacteriol. 2012; 194(24):6930-1. PMC: 3510619. DOI: 10.1128/JB.01828-12. View

15.

Schofl G, Voigt A, Litsche K, Sachse K, Peter Saluz H . Complete genome sequences of four mammalian isolates of Chlamydophila psittaci. J Bacteriol. 2011; 193(16):4258. PMC: 3147682. DOI: 10.1128/JB.05382-11. View

16.

Walker B, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S . Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014; 9(11):e112963. PMC: 4237348. DOI: 10.1371/journal.pone.0112963. View